I had the same problem. Checking the 32-bit runtime box still sometimes didn't result in it actually "sticking." I found that I had to actually alter the job step to add the proper '/X86' syntax to the command. I actually tested this by checking the box and then scripting the job - still no 32-bit option set! I honestly think there is a bug in the 2012 GUI for setting up the job step, but in any case, try this:

Right-click the job, choose Script Job...check out the section for the SSIS job step. Look at the @command piece. You SHOULD see '/X86' after the server name and before the '/Par' (see below).

If you don't, you can copy the whole line, ADD the '/X86' and then modify the job...like this:

EXEC dbo.sp_update_jobstep

@job_name = N'MyJOBName',

@step_id = 1,

@command=N'/ISSERVER "\"\SSISDB\MyPackage.dtsx\"" /SERVER "\"MyServer\"" /X86 /Par "\"$ServerOption::LOGGING_LEVEL(Int16)\"";1 /Par "\"$ServerOption::SYNCHRONIZED(Boolean)\"";True /CALLERINFO SQLAGENT /REPORTING E'

GO